https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/ Issue: sci-biology/abyss-2.0.3-r2 fails to compile. Discovered on: amd64 (internal ref: tinderbox) NOTE: This machine uses a clang/LLVM toolchain. If you think that this issue is strictly related to clang/LLVM please block bug 408963. If you think that this issue is strictly related to the LLD linker, please block bug 731004. This machine uses also GLIBC-2.32. If you think that this issue is strictly related to GLIBC please block bug 736174.
Created attachment 659128 [details] build.log build log and emerge --info
Probably related to clang (or newer c++ standard in general): """ x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3-r2/work/abyss-2.0.3 -isystem/var/tmp/portage/sci-biology/abyss-2.0.3-r2/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc In file included from Histogram.cpp:1: ./Histogram.h:315:14: error: 'swap<Histogram>' is missing exception specification 'noexcept(__and_<is_nothrow_move_constructible<Histogram>, is_nothrow_move_assignable<Histogram> >::value)' inline void swap(Histogram&, Histogram&) { assert(false); } ^ noexcept(__and_<is_nothrow_move_constructible<Histogram>, is_nothrow_move_assignable<Histogram> >::value) ./Histogram.h:315:14: note: previous declaration is here 1 error generated. make[2]: *** [Makefile:473: libcommon_a-Histogram.o] Error 1 """
I think it's fixed upstream a while ago in https://github.com/bcgsc/abyss/commit/b1bc50be8a3a2038c68b5599e98cdeafe9e2df23 by forcing c++11 and is available in newer versions of abyss. Version bump should be enough.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=89ab6a3d9d32bcb93e27580298094a875a530685 commit 89ab6a3d9d32bcb93e27580298094a875a530685 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-01-13 11:20:26 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-01-13 11:21:37 +0000 sci-biology/abyss: drop version 2.0.3 Closes: https://bugs.gentoo.org/741154 Closes: https://bugs.gentoo.org/715718 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/abyss/Manifest | 1 - sci-biology/abyss/abyss-2.0.3-r2.ebuild | 64 ----------------------- sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 ---- 3 files changed, 76 deletions(-)
